One thing that I’ve found interesting is how ignorant many people – even many biologists! – are about the mutational processes in the cell. The idea that mutations come from copying “errors” is so embedded in our collective consciousness, that it is hard to get people to even fathom alternatives.
Thinking of mutation as a biological process – one under the organization/direction of the cell – leads to a lot of interesting biology. There are indeed copying errors, but my guess is that by the end of the century we will find that the ones that are actually errors are by far the least numerous. This is like the discovery of microbes. We first found them *because* they caused disease. Therefore, our first reaction was that microbes *are* diseased. But later we find out that >99% of them are actually good for us and the environment, and there are just a handful that are problematic.
Normally, DNA is copied by DNA Polymerase III. Yes, there are more than one DNA polymerase gene! Why, you ask? That’s because DNA Polymerase III is a “high-fidelity” polymerase, basically making exact copies. But, if the cell detects that it *needs* mutations, it switches to a SEPARATE GENE, whose function is to copy DNA *while inserting* mutations!
So, in E. coli, the “SOS response” system is well-studied. In this system, when E. coli is stressed (lack of food, etc.), it tries to alter its own physiology by inducing mutations. It switches from the high-fidelity DNA Polymerase III to one of the other polymerases (II, IV, or V), which induce various mutations. It also makes lots of copies of its metabolism genes using these polymerases, since these are the genes most likely to confer benefit from mutating if the organism is starving.
Then, when a mutation is found that relieves the stress, it turns off the mutation-inducing polymerase, and goes back to DNA Polymerase III to get high-fidelity copies of the new gene.
So, as you can see, the Darwinian view of “random mutations” is simply false. The organism has SEPARATE genes for creating mutations, and invokes them when it has need of mutations, and focuses mutations on the genes that are likely to yield benefits.